cwlVersion: v1.1
class: Workflow
-label: Variant calling workflow for single interval
+label: Variant calling workflow for given interval
requirements:
- class: SubworkflowFeatureRequirement
inputs:
bam:
type: File
+ format: edam:format_2572 # BAM
+ label: Indexed sorted BAM with labeled duplicates
secondaryFiles:
- .bai
reference:
type: File
+ format: edam:format_1929 # FASTA
+ label: Reference genome
secondaryFiles:
- .amb
- .ann
- .sa
- .fai
- ^.dict
- sample: string
- knownsites1:
+ sample:
+ type: string
+ label: Sample Name
+ knownsites:
type: File
+ format: edam:format_3016 # VCF
+ label: VCF of known polymorphic sites for BQSR
secondaryFiles:
- .tbi
intervallist:
type: File
+ label: Scatter intervals file
outputs:
gvcf:
type: File
+ format: edam:format_3016 # GVCF
+ label: Given interval filtered GVCF
outputSource: selectvariants/filteredgvcf
steps:
bam: bam
reference: reference
sample: sample
- knownsites1: knownsites1
+ knownsites: knownsites
intervallist: intervallist
out: [recaltable]
applyBQSR:
run: gatk-applyBSQR-with-interval.cwl
- in:
+ in:
reference: reference
bam: bam
sample: sample
out: [gvcf]
selectvariants:
run: gatk-selectvariants.cwl
- in:
+ in:
gvcf: haplotypecaller/gvcf
reference: reference
sample: sample
s: https://schema.org/
edam: http://edamontology.org/
-$schemas:
- - https://schema.org/version/latest/schema.rdf
- - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+# - https://schema.org/version/latest/schema.rdf
+# - http://edamontology.org/EDAM_1.18.owl